Analyzing the effects of DMARD treatment on genetic expression
Background Information
What are the genome-wide transcriptional effects in RA (rheumatoid arthritis) patients who are undergoing treatment with several disease-modifying drugs (DMARDs)?
Multiple biological pathways are likely impacted by DMARD, but specifics of the pathways are unknown.
Study’s findings
From the 8000 analyzed genes, < 300 had a reversed gene expression as a result of DMARD therapy. These genes are related to the immune system, and largely expressed by lymphocytes.
Project purpose
What are the genetic differences in RA patients, before and after DMARD treatment?
Identify genes or molecular pathways that are influenced.
Identify relevant treatment targets, with their respective molecular pathway(s).
Preparing the data
Supplementary tables 1 and 3, containing co-expression modules, and genetic expression of regulator molecules, respectively.
Two separate parts of table 3, split into “before” and “after treatment”.
Wrangling the data
In order to perform analysis, the data was split, pivoted, joined.
Redundant data was removed.
Augmenting the data
Adding a class variable, to distinguish between the upstream regulators, which are significantly expressed and which are not.
Furthermore, significant regulator molecules were characterized as genetic up- and down-regulated.
Dimensions of the data
“expr_before”: Expression profile before treatment.
“expr_after”: Expression profile after treatment.
“expr_intersect”: In common regulators, before and after treatment.
“target_intersect”: Target molecules, affected by regulator expression.
“coexpression”: Overview of related molecular pathways.
Differential expressed regulators
From the data in table 1 and 2, it can be seen that there is a difference in regulator expression before and after treatment.
Differential expressed regulator molecules
To visualize the genetic up- and down-regulation, two volcano plots were made. These plots indicate the differences in genetic expression before and after DMARD treatment, respectively.
Differential expressed regulators before treatment
First, the plot below shows the genetic expression levels in RA patients, before DMARD treatment.
Differential expressed regulators after treatment
Secondly, we show genetic expression levels in RA patients, after DMARD treatment.
Differential expressed regulators after treatment
Lastly, we show a comparison plot to indicate genetic differences as a result of treatment.
Target molecules
The upstream regulators consisted of several types of biological molecules, serving various functions.
Target molecules
The upstream regulators each influence several target molecules. To analyze which regulators had the most severe impact on molecular pathways, we plot the number of target molecules, affected by each regulator.
Target molecules
Target molecules
The regulators S100A9, TGFB1, and TLR2, are found to undergo significant expression changes due to DMARD treatment.
Whether or not these genes have a sufficient impact on RA prognosis, depends on the molecular pathway they play a role in. Therefore, we analyzed which molecular mechanisms the gene is involved in.
Molecular mechanisms related to the most influential genes
A module is a cluster of related genes, either with related function, common transcriptional regulation, or selectively co-expressed in certain cell types.
Molecular mechanisms related to the most influential genes
From this plot, TGFB1 can be a potential drug target.
Findings from the study
The study by Walsh et.al. found 292 genes down-regulated due to treatment, and 23 up-regulated. The down regulated genes are related to the immune system, a.o. T-cell activating-genes.
This can be explained due to the fact that RA is an auto-immune disease. Less disease activity means less immune activity, and vice versa.
The genetic regulation is based on RA patients, compared to healthy control samples.
Our findings
We identified TGFB1 as a potential drug target.
This finding is based on RA patients before and after DMARD treatment.
TGFB1, and its corresponding “module 2” molecules, are potential drug targets for further investigation.